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<p>During analyzing experiment data, we’ve found that many data
analysis processes are identical. In an effort to save time and labor,
we’ve written down some scripts to deal with large data sets of a
similar group or from a similar experiment. We’re posting our codes here
in the hope that when someone else in the future has to deal with data
sets from a similar experiment, our codes would help to make such
processes easier. Moreover, we believe that tools can make synthetic
biology more standardized than ever.</p>
<p>&nbsp;&nbsp;Characterization is undoubtedly both common and
important in synthetic biology. Though there’re more than one way to
characterize promoter activity, the usage of fluorescence protein (such
as GFP, YFP, RFP and CFP) is quick and convenient. One can attach the
coding region of GFP for instance to the promoter (including RBS) and
measure the fluorescence intensity.</p>
<p>&nbsp;&nbsp;The tools we offer here can be used to analyze the
data collected (OD and fluorescence time profile) and compute the
transcription rate (PoPS). We’ve written one function file for matlab
and another Macro for Excel. The codes have been thoroughly documented,
making it much easier to use and modify. For more information on
detailed experiment steps for characterization, please refer to our
biobrick characterization page and protocol.</p>
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<p>&nbsp;&nbsp;The transcription rate can be calculated by the
following function (Leveau and Lindow, 2001):</p>
<p><img src="http://2011.igem.org/wiki/images/1/1c/Zjutools.png"
	/ width="700"></p>
<p>&nbsp;&nbsp;P=transcription rate(PoPS); μ=growth rate; m=XFP
maturation; D=XFP degradation; fss=steady-state fluorophore
concentration at exponential phase. The default vaules for m (1.5h-1,
Andersen et al.,1998) and D (0.23h-1, Cormack et al.,1996) are for GFP
as the reporter.</p>
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<p>&nbsp;&nbsp;The output consists of 1 value of PoPS and 4 figures
automatically saved under the current directory. The output for the
example is as follows:</p>
<blockquote>
<h1 style="text-align: center"><strong>PoPS = 2.3546e4</strong> /h</h1>
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<p><strong>>><a
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function file</a></strong><a
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